Add visfAtlas

[marcobarilari]

• update README
• test

[codecov]

Codecov Report

Merging #38 (3786bb0) into dev (d9910b3) will increase coverage by 0.89%.
The diff coverage is 87.50%.

@@            Coverage Diff             @@
##              dev      #38      +/-   ##
==========================================
+ Coverage   88.14%   89.03%   +0.89%     
==========================================
  Files          20       20              
  Lines         371      383      +12     
==========================================
+ Hits          327      341      +14     
+ Misses         44       42       -2     

Flag	Coverage Δ
unittests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/atlas/extractRoiFromAtlas.m	81.25% <77.77%> (-2.75%)	⬇️
src/atlas/getAtlasFilename.m	81.81% <100.00%> (+1.81%)	⬆️
src/atlas/getLookUpTable.m	42.85% <100.00%> (+6.01%)	⬆️
src/atlas/unzipAtlas.m	100.00% <100.00%> (ø)
src/utils/removePrefix.m	100.00% <0.00%> (+100.00%)	⬆️

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[Remi-Gau]

for the tests:

Maybe add one in here:

• https://github.com/cpp-lln-lab/CPP_ROI/blob/dev/tests/test_getLookUpTable.m
• https://github.com/cpp-lln-lab/CPP_ROI/blob/dev/tests/test_extractRoiFromAtlas.m

[marcobarilari]

There is one test failing but I have no idea what it means. The rest should be GTG

[Remi-Gau]

there is a typo and I would easily remove lots of stuff from their README: it may be confusing to our users otherwise (they mention some xml but it is not shipped with CPP ROI)

[Remi-Gau]

for the tests, the reports in CI are a bit hidden.

they start here at the end of the run_command step

https://github.com/cpp-lln-lab/CPP_ROI/runs/6471860906?check_suite_focus=true#step:7:143

FAILED (failure=7, passed=24)

fyi those tests run super quickly so definitely worth trying them locally

[Remi-Gau]

That should fix a few tests

The other ones seem to be more bids-matlab related

Let me investigate

[Remi-Gau]

I have fixed some tests that were due to a bids-matlab update, there is another one failing that might need a fix on the bids matlab front

[Remi-Gau]

  --------------------------------------------------
  
  failure: Error using getLookUpTable (line 24)
  unknown atlas type
    getLookUpTable:24 (/tmp/tpf88e232a_eb19_4c75_b4fa_782644e1d205/atlas/getLookUpTable.m)
    getAtlasAndLut:8 (/tmp/tpf88e232a_eb19_4c75_b4fa_782644e1d205/atlas/getAtlasAndLut.m)
    extractRoiFromAtlas:27 (/tmp/tpf88e232a_eb19_4c75_b4fa_782644e1d205/atlas/extractRoiFromAtlas.m)
    test_extractRoiFromAtlas_visfAtlas:46 (/home/runner/work/CPP_ROI/CPP_ROI/tests/test_extractRoiFromAtlas.m)
  
  failure: Error using getLookUpTable (line 24)
  unknown atlas type
    getLookUpTable:24 (/tmp/tpf88e232a_eb19_4c75_b4fa_782644e1d205/atlas/getLookUpTable.m)
    test_lut_visfAtlas:48 (/home/runner/work/CPP_ROI/CPP_ROI/tests/test_getLookUpTable.m)
  
  --------------------------------------------------
  
  FAILED (passed=29, failure=2)

OK I pushed some change on bids matlab so now all the remaining failing tests should be fixable within this repo only